Improved reference genome of Aedes aegypti informs arbovirus vector control

Nature, Journal Year: 2018, Volume and Issue: 563(7732), P. 501 - 507

Published: Nov. 14, 2018

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of developing tools to fight them has been slowed by lack a high-quality genome assembly. Here we combine diverse technologies produce markedly improved, fully re-annotated AaegL5 assembly, demonstrate how it accelerates mosquito science. We anchored physical cytogenetic maps, doubled number known chemosensory ionotropic receptors that guide human hosts egg-laying sites, provided further insight into size composition sex-determining M locus, revealed copy-number variation among glutathione S-transferase genes are important for insecticide resistance. Using high-resolution quantitative trait locus population genomic analyses, mapped new candidates dengue vector competence will catalyse biological insights intervention strategies this deadly disease vector.

Language: Английский

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Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Nature Plants, Journal Year: 2020, Volume and Issue: 6(3), P. 259 - 272

Published: March 13, 2020

Abstract Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including distinct sporophyte architecture, cyanobacterial symbiosis pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as sister clade to liverworts plus mosses with high support. The lack repeat-dense centromeres well whole-genome duplication, contain limited transcription factor repertoire. Several genes involved in angiosperm meristem stomatal function are conserved upregulated during development, suggesting possible homologies at the genetic level. We identified candidate found LCIB , Chlamydomonas CCM gene, is present but absent plant lineages, implying role function. anticipate these hornwort will serve essential references for future research comparative studies across plants.

Language: Английский

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Ancient gene linkages support ctenophores as sister to other animals

Nature, Journal Year: 2023, Volume and Issue: 618(7963), P. 110 - 117

Published: May 17, 2023

Abstract A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for evolution of complex neural systems and animal-specific traits 1–6 . Conventional approaches based on morphological characters increasingly extensive gene sequence collections have not been able definitively answer this 7–11 Here we develop chromosome-scale linkage, also known as synteny, a character resolving 12 We report new genomes ctenophore two marine sponges, three unicellular relatives animals (a choanoflagellate, filasterean amoeba an ichthyosporean) that serve outgroups analysis. find ancient syntenies conserved between their close relatives. Ctenophores eukaryotes share ancestral metazoan patterns, whereas bilaterians, cnidarians derived chromosomal rearrangements. Conserved syntenic unite with cnidarians, placozoans monophyletic clade exclusion ctenophores, placing The patterns synteny shared by result rare irreversible chromosome fusion-and-mixing events provide robust unambiguous support ctenophore-sister hypothesis. findings framework deep, recalcitrant problems implications our understanding animal evolution.

Language: Английский

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Construction of a chromosome-scale long-read reference genome assembly for potato

GigaScience, Journal Year: 2020, Volume and Issue: 9(9)

Published: Sept. 1, 2020

Worldwide, the cultivated potato, Solanum tuberosum L., is No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, doubled monoploid clone S. Group Phureja, was published in 2011 using whole-genome shotgun sequencing approach with short-read data. Current advanced technologies now permit generation near-complete, high-quality chromosome-scale assemblies at minimal cost.Here, we present an updated version R44 (v6.1) Oxford Nanopore Technologies long reads coupled proximity-by-ligation scaffolding (Hi-C), yielding assembly. new assembly represents 741.6 Mb (87.8%) estimated 844 genome, which 741.5 non-gapped 731.2 anchored to 12 chromosomes. Use full-length complementary DNA enabled annotation 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had significantly improved representation conserved orthologs compared previous annotation. has contiguity 595-fold increase N50 contig size, 99% reduction number contigs, 44-fold scaffold LTR Assembly Index score 13.56, placing it category reference quality. also permitted centromeres via alignment derived from CENH3 nucleosomes.Access software high-quality, long-read, dataset for genotype potato will facilitate research aimed improving agronomic traits understanding evolution.

Language: Английский

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Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

Current Biology, Journal Year: 2020, Volume and Issue: 30(4), P. 573 - 588.e7

Published: Jan. 30, 2020

Genome packaging by nucleosomes is a hallmark of eukaryotes. Histones and the pathways that deposit, remove, read histone modifications are deeply conserved. Yet, we lack information regarding chromatin landscapes in extant representatives ancestors main groups eukaryotes, our knowledge evolution chromatin-related processes limited. We used bryophyte Marchantia polymorpha, which diverged from vascular plants circa 400 mya, to obtain whole chromosome genome assembly explore landscape three-dimensional organization an early diverging land plant lineage. Based on genomic profiles ten marks, conclude relationship between active marks gene expression conserved across plants. In contrast, observed distinctive features transposons other repetitive sequences compared with flowering Silenced repeats did not accumulate around centromeres. Although large fraction constitutive heterochromatin was marked H3K9 methylation as plants, significant proportion were H3K27me3, otherwise dedicated transcriptional repression protein-coding genes Chromatin compartmentalization analyses Hi-C data revealed repressed B compartments densely decorated H3K27me3 but or DNA reported that, played essential role function, suggesting ancestral this mark transposon silencing.

Language: Английский

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Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Nov. 7, 2019

Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct nuclei). Newly emerged strains the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, a major threat global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation nuclear between dikaryons. Fully haplotype-resolved genome assembly DNA proximity analysis reveal shares one nucleus genotype with much older African lineage Pgt, no recombination or chromosome reassortment. These findings indicate dikaryotes can generate facilitate emergence new lineages asexual fungal populations.

Language: Английский

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High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads

Genomics Proteomics & Bioinformatics, Journal Year: 2021, Volume and Issue: 20(1), P. 4 - 13

Published: Sept. 3, 2021

Abstract Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, genomics. However, the latest version of reference genome still contains a significant number missing segments. Here, we reported high-quality almost complete Col-0 assembly with two gaps (named Col-XJTU) by combining Oxford Nanopore Technologies ultra-long reads, Pacific Biosciences high-fidelity long Hi-C data. The total size 133,725,193 bp, introducing 14.6 Mb novel sequences compared to TAIR10.1 genome. All five chromosomes Col-XJTU are highly accurate consensus quality (QV) scores > 60 (ranging from 62 68), which higher than those 45 52). We completely resolved chromosome (Chr) 3 Chr5 in telomere-to-telomere manner. Chr4 was except nucleolar organizing regions, comprise repetitive DNA fragments. Chr1 centromere (CEN1), reportedly around 9 length, particularly challenging assemble due presence tens thousands CEN180 satellite repeats. Using cutting-edge sequencing data computational approaches, assembled 3.8-Mb-long CEN1 3.5-Mb-long CEN2. also investigated structure epigenetics centromeres. Four clusters monomers were detected, centromere-specific histone H3-like protein (CENH3) exhibited strong preference Cluster 3. Moreover, observed hypomethylation patterns CENH3-enriched regions. believe that this assembly, Col-XJTU, would serve as valuable better understand global pattern centromeric polymorphisms, well genetic epigenetic features plants.

Language: Английский

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StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

Bioinformatics, Journal Year: 2022, Volume and Issue: 38(7), P. 2049 - 2051

Published: Jan. 7, 2022

Abstract Summary The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence telomere-to-telomere assemblies with multi-megabase requires new strategies. Here, we introduce StainedGlass, which can generate publication-quality figures interactive visualizations that depict identity orientation tandem repeat structures at a genome-wide scale. tool rapidly reveal higher-order improve inference evolutionary history for some most complex regions genomes. Availability implementation StainedGlass implemented Snakemake available open source under MIT license https://mrvollger.github.io/StainedGlass/. Supplementary information data are Bioinformatics online.

Language: Английский

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Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 20, 2024

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history capsaicinoid biosynthesis and mechanism their tissue specificity remain obscure lack high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes C. annuum wild nonpungent relative rhomboideum investigate evolution in chili peppers. We precisely delineate centromeres, which high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, estimate timing biosynthesis. reveal disrupted coding regulatory regions key genes species. also find conserved placenta-specific accessible chromatin regions, likely allow tissue-specific biosynthetic gene coregulation accumulation. These T2T genomic resources will accelerate genetic improvement help understand genome evolution.

Language: Английский

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(1), P. 263 - 286

Published: Sept. 16, 2020

Abstract Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs increasing efficiency of sequencing technologies now enable assembling genomes unprecedented quality contiguity. However, the difficulty in repeat‐rich GC‐rich regions (genomic “dark matter”) limits insights into evolution genome structure regulatory networks. Here, we compare available (short/linked/long reads proximity ligation maps) combinations thereof genomic dark matter. By adopting different de novo assembly strategies, draft to a curated multiplatform reference identify features that cause gaps within each assembly. We show implementing long‐read, linked‐read performs best recovering transposable elements, multicopy MHC genes, microchromosomes W chromosome. Telomere‐to‐telomere not reality yet for most organisms, but leveraging technology choice it is possible minimize downstream analysis. provide roadmap tailor projects optimized completeness both coding noncoding parts nonmodel genomes.

Language: Английский

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